Different gene rearrangements of the genus Dardanus (Anomura: Diogenidae) and insights into the phylogeny of Paguroidea

AbstractComplete mitochondrial genomes (mitogenomes) can provide useful information for phylogenetic relationships, gene rearrangement, and molecular evolution. In this study, the complete mitogenomes of two hermit crabs, Dardanus arrosor and Dardanus aspersus, were sequenced for the first time and compared with other published mitogenomes of Paguroidea. Each of the two mitogenomes contains an entire set of 37 genes and a putative control region, but they display different gene arrangements. The different arrangements of the two mitogenomes might be the result of transposition, reversal, and tandem duplication/random loss events from the ancestral pancrustacean pattern. Genome sequence similarity analysis reveals the gene rearrangement in 15 Paguroidea mitogenomes. After synteny analysis between the 15 Paguroidea mitogenomes, an obvious rearranged region is found in D. aspersus mitogenome. Across the 13 protein-coding genes (PCGs) tested, COI has the least and ND6 has the largest genetic distances among the 15 hermit crabs, indicating varied evolution rates of PCGs. In addition, the dN/dS ratio analysis shows that all PCGs are evolving under purifying selection. The phylogenetic analyses based on both gene order and sequence data present the monophyly of three families (Paguridae, Coenobitidae, and Pylochelidae) and the paraphyly of the family Diogenidae. Meanwhile, the phylogenetic tree based on the nucleotide sequences of 13 PCGs shows that two Dardanus species formed a sister group with five Coenobitidae species. These findings help to better understand the gene rearrangement and phylogeny of Paguroidea, as well as provide new insights into the usefulness of mitochondrial gene order as a phylogenetic marker.

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Diversification of the North American Doellingeria-Eucephalus Clade (Astereae: Asteraceae) Inferred from Molecular and Morphological Evidence

Systematic Botany ◽

10.1600/036364419x15710776741477 ◽

2019 ◽

Vol 44 (4) ◽

pp. 930-942

Author(s):

Geraldine A. Allen ◽

Luc Brouillet ◽

John C. Semple ◽

Heidi J. Guest ◽

Robert Underhill

Keyword(s):

North American ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Sister Group ◽

Morphological Evidence ◽

South American ◽

New Combinations ◽

The North ◽

Hybridization Event ◽

Ancient Hybridization

Abstract—Doellingeria and Eucephalus form the earliest-diverging clade of the North American Astereae lineage. Phylogenetic analyses of both nuclear and plastid sequence data show that the Doellingeria-Eucephalus clade consists of two main subclades that differ from current circumscriptions of the two genera. Doellingeria is the sister group to E. elegans, and the Doellingeria + E. elegans subclade in turn is sister to the subclade containing all remaining species of Eucephalus. In the plastid phylogeny, the two subclades are deeply divergent, a pattern that is consistent with an ancient hybridization event involving ancestral species of the Doellingeria-Eucephalus clade and an ancestral taxon of a related North American or South American group. Divergence of the two Doellingeria-Eucephalus subclades may have occurred in association with northward migration from South American ancestors. We combine these two genera under the older of the two names, Doellingeria, and propose 12 new combinations (10 species and two varieties) for all species of Eucephalus.

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Not Frozen in the Ice: large and Dynamic Rearrangements in the Mitochondrial Genomes of the Antarctic Fish

Genome Biology and Evolution ◽

10.1093/gbe/evab017 ◽

2021 ◽

Author(s):

Chiara Papetti ◽

Massimiliano Babbucci ◽

Agnes Dettai ◽

Andrea Basso ◽

Magnus Lucassen ◽

...

Keyword(s):

Gene Order ◽

Hot Spot ◽

Mitochondrial Gene ◽

Antarctic Fish ◽

Purifying Selection ◽

Compositional Bias ◽

Mitochondrial Genomes ◽

Notothenioid Fish ◽

Antarctic Notothenioids ◽

The Antarctic

Abstract The vertebrate mitochondrial genomes generally present a typical gene order. Exceptions are uncommon and important to study the genetic mechanisms of gene order rearrangements and their consequences on phylogenetic output and mitochondrial function. Antarctic notothenioid fish carry some peculiar rearrangements of the mitochondrial gene order. In this first systematic study of 28 species, we analysed known and undescribed mitochondrial genome rearrangements for a total of eight different gene orders within the notothenioid fish. Our reconstructions suggest that transpositions, duplications and inversion of multiple genes are the most likely mechanisms of rearrangement in notothenioid mitochondrial genomes. In Trematominae, we documented an extremely rare inversion of a large genomic segment of 5300 bp that partially affected the gene compositional bias but not the phylogenetic output. The genomic region delimited by nad5 and trnF, close to the area of the Control Region, was identified as the hot spot of variation in Antarctic fish mitochondrial genomes. Analysing the sequence of several intergenic spacers and mapping the arrangements on a newly generated phylogeny showed that the entire history of the Antarctic notothenioids is characterized by multiple, relatively rapid, events of disruption of the gene order. We hypothesised that a pre-existing genomic flexibility of the ancestor of the Antarctic notothenioids may have generated a precondition for gene order rearrangement, and the pressure of purifying selection could have worked for a rapid restoration of the mitochondrial functionality and compactness after each event of rearrangement.

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Mitochondrial Genomes from Two Specialized Subfamilies of Reduviidae (Insecta: Hemiptera) Reveal Novel Gene Rearrangements of True Bugs

Genes ◽

10.3390/genes12081134 ◽

2021 ◽

Vol 12 (8) ◽

pp. 1134

Author(s):

Fei Ye ◽

Hu Li ◽

Qiang Xie

Keyword(s):

Gene Rearrangement ◽

Hot Spot ◽

Phylogenetic Analyses ◽

Mitochondrial Gene ◽

Deep Understanding ◽

Gene Arrangement ◽

Mitochondrial Genomes ◽

Current View ◽

Novel Gene ◽

Spot Group

Reduviidae, a hyper-diverse family, comprise 25 subfamilies with nearly 7000 species and include many natural enemies of crop pests and vectors of human disease. To date, 75 mitochondrial genomes (mitogenomes) of assassin bugs from only 11 subfamilies have been reported. The limited sampling of mitogenome at higher categories hinders a deep understanding of mitogenome evolution and reduviid phylogeny. In this study, the first mitogenomes of Holoptilinae (Ptilocnemus lemur) and Emesinae (Ischnobaenella hainana) were sequenced. Two novel gene orders were detected in the newly sequenced mitogenomes. Combined 421 heteropteran mitogenomes, we identified 21 different gene orders and six gene rearrangement units located in three gene blocks. Comparative analyses of the diversity of gene order for each unit reveal that the tRNA gene cluster trnI-trnQ-trnM is the hotspot of heteropteran gene rearrangement. Furthermore, combined analyses of the gene rearrangement richness of each unit and the whole mitogenome among heteropteran lineages confirm Reduviidae as a ‘hot-spot group’ of gene rearrangement in Heteroptera. The phylogenetic analyses corroborate the current view of phylogenetic relationships between basal groups of Reduviidae with high support values. Our study provides deeper insights into the evolution of mitochondrial gene arrangement in Heteroptera and the early divergence of reduviids.

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Mitogenome of Alaudala cheleensis (Passeriformes: Alaudidae) and comparative analyses of Sylvioidea mitogenomes

Zootaxa ◽

10.11646/zootaxa.4952.2.7 ◽

2021 ◽

Vol 4952 (2) ◽

pp. 331-353

Author(s):

CHAO YANG ◽

LE ZHAO ◽

QINGXIONG WANG ◽

HAO YUAN ◽

XUEJUAN LI ◽

...

Keyword(s):

Secondary Structure ◽

Gene Order ◽

Phylogenetic Relationships ◽

Gene Rearrangement ◽

Phylogenetic Analyses ◽

Protein Coding ◽

Comparative Analyses ◽

Protein Coding Genes ◽

Basal Position

To gain a better understanding of mitogenome features and phylogenetic relationships in Sylvioidea, a superfamily of Passerida, suborder Passeri, Passeriformes, the whole mitogenome of Alaudala cheleensis Swinhoe (Alaudidae) was sequenced, a comparative mitogenomic analysis of 18 Sylvioidea species was carried out, and finally, a phylogeny was reconstructed based on the mitochondrial dataset. Gene order of the A. cheleensis mitogenome was similar to that of other Sylvioidea species, including the gene rearrangement of cytb-trnT-CR1-trnP-nad6-trnE-remnant CR2-trnF-rrnS. There was slightly higher A+T content than that of G+C in the mitogenome, with an obvious C skew. The ATG codon initiated all protein-coding genes, while six terminating codons were used. The secondary structure of rrnS contained three domains and 47 helices, whereas rrnL included six domains and 60 helices. All tRNAs could be folded into a classic clover-leaf secondary structure except for trnS (AGY). The CR1 could be divided into three domains, including several conserved boxes (C-string, F, E, D, C and B-box, Bird similarity box, CSB1). Comparative analyses within Sylvioidea mitogenomes showed that most mitochondrial features were consistent with that of the A. cheleensis mitogenome. The basal position of the Alaudidae within the Sylvioidea in our phylogenetic analyses is consistent with other recent studies.

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Mimaporia, a new genus of Epicopeiidae (Lepidoptera), with description of a new species from Vietnam

Zootaxa ◽

10.11646/zootaxa.4254.5.3 ◽

2017 ◽

Vol 4254 (5) ◽

pp. 537 ◽

Cited By ~ 5

Author(s):

CHIA-HSUAN WEI ◽

SHEN-HORN YEN

Keyword(s):

New Species ◽

New Genus ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Taxonomic Status ◽

Sister Group ◽

Morphological Evidence ◽

New Taxon ◽

The Family ◽

A New Species

The Epicopeiidae is a small geometroid family distributed in the East Palaearctic and Oriental regions. It exhibits high morphological diversity in body size and wing shape, while their wing patterns involve in various complex mimicry rings. In the present study, we attempted to describe a new genus, and a new species from Vietnam, with comments on two assumed congeneric novel species from China and India. To address its phylogenetic affinity, we reconstructed the phylogeny of the family by using sequence data of COI, EF-1α, and 28S gene regions obtained from seven genera of Epicopeiidae with Pseudobiston pinratanai as the outgroup. We also compared the morphology of the new taxon to other epicopeiid genera to affirm its taxonomic status. The results suggest that the undescribed taxon deserve a new genus, namely Mimaporia gen. n. The species from Vietnam, Mimaporia hmong sp. n., is described as new to science. Under different tree building strategies, the new genus is the sister group of either Chatamla Moore, 1881 or Parabraxas Leech, 1897. The morphological evidence, which was not included in phylogenetic analyses, however, suggests its potential affinity with Burmeia Minet, 2003. This study also provides the first, although preliminary, molecular phylogeny of the family on which the revised systematics and interpretation of character evolution can be based.

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A revision of the planthopper genus Chionomus Fennah (Hemiptera: Fulgoroidea: Delphacidae)

Zootaxa ◽

10.11646/zootaxa.4811.1.1 ◽

2020 ◽

Vol 4811 (1) ◽

pp. 1-63

Author(s):

KATHRYN M. WEGLARZ ◽

CHARLES R BARTLETT

Keyword(s):

Mixed Model ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Mitochondrial Gene ◽

Molecular Evidence ◽

Additional Species ◽

Molecular Sequence Data ◽

Molecular Sequence ◽

Original Definition ◽

Definition Of

The planthopper genus Chionomus Fennah, 1971 (Hemiptera: Fulgoroidea: Delphacidae) currently includes three Neotropical species, removed from the polyphyletic genus Delphacodes Fieber, 1866. Morphological and molecular evidence further redefine Chionomus to include ten additional species (eight species removed from Delphacodes, two described as new, viz. Chionomus dolonus n. sp. and C. herkos n. sp.), with another four species synonymized. Phylogenetic analyses of morphological and molecular sequence data of the mitochondrial gene Cytochrome Oxidase I provide support for the monophyly of Chionomus. We use a mixed model Bayesian optimality criterion to define phylogenetic relationships among Chionomus and support paraphyly of the original definition of Chionomus (with respect to Delphacodes) and monophyly of the revised genus.

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The description of a cryptic species related to the pan-Amazonian frog Allobates femoralis (Boulenger 1883) (Anura: Aromobatidae)

Zootaxa ◽

10.11646/zootaxa.2406.1.1 ◽

2010 ◽

Vol 2406 (1) ◽

pp. 1 ◽

Cited By ~ 21

Author(s):

PEDRO IVO SIMÕES ◽

ALBERTINA P. LIMA ◽

IZENI PIRES FARIAS

Keyword(s):

New Species ◽

Phylogenetic Analyses ◽

Mitochondrial Gene ◽

Sister Group ◽

Sensu Stricto ◽

Left Bank ◽

Genetic Introgression ◽

Nucleotide Substitutions ◽

Advertisement Calls ◽

Allobates Femoralis

We describe a new species of litter frog from western Brazilian Amazon previously referred to as Allobates femoralis (Boulenger 1883). The new species is allopatric to A. femoralis and its known occurrence is restricted to terra-firme forests on the left bank of the upper Madeira River and southeastern State of Acre. This species is distinguished from A. femoralis and from other species in the A. femoralis group by presenting two-note advertisement calls and conspicuous reddish-orange color on ventral surfaces of hind limbs and posterior abdomen. Phylogenetic analyses based on a fragment of the 16S rRNA mitochondrial gene suggest the new species is the sister group to a clade referred to as A. femoralis occurring in southern State of Acre, from which it is distinguished by six unambiguous nucleotide substitutions, in addition to exclusive advertisement calls and color patterns. The new species is more distantly related to A. femoralis sensu stricto occurring near the A. femoralis type locality in the Peruvian Amazon. Summarizing evidence from molecular phylogenetic analysis, genetic distances and available data on advertisement calls, we identify one possible case of genetic introgression between lineages in this group and highlight the potential for the description of more species within the A. femoralis complex.

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Genetic diversity, species phylogeny and historical biogeography of the Aquarius paludum group (Heteroptera: Gerridae)

Insect Systematics & Evolution ◽

10.1163/187631203788964791 ◽

2003 ◽

Vol 34 (3) ◽

pp. 313-327 ◽

Cited By ~ 18

Author(s):

Herbert Zettel ◽

Jakob Damgaard

Keyword(s):

Genetic Diversity ◽

Sequence Data ◽

Mitochondrial Gene ◽

Taxonomic Status ◽

Species Group ◽

Genetic Distances ◽

The Philippines ◽

Disjunct Distribution ◽

Gene Encoding ◽

Vicariance Event

AbstractWe investigated genetic diversity and phylogeny of all water strider species assigned to the Aquarius paludum species group on basis of 425 bp DNA sequence data from the mitochondrial gene encoding cytochrome oxidase subunit I (COI). Parsimony analyses and genetic distances confirmed the taxonomic status of the two recently described species Aquarius lili Polhemus & Polhemus, 1994 from Timor and A. philippinensis Zettel & Ruiz, 2003 from the Philippines as being separate from the widespread Oriental A. adelaidis (Dohrn, 1860). Molecular clock estimates suggest that the disjunct zoogeographical pattern among the three species is due to a Pliocene/Pleistocene long-range dispersal, rather than a Mesozoic vicariance event as previously suggested. However, when we superimposed the disjunct distribution of Southern Hemisphere representatives of the paludum-group onto their phylogenetic relationship, the pattern indicated vicariance events following the break-up of Gondwana.

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Single molecule, near full-length genome sequencing of dengue virus

Scientific Reports ◽

10.1038/s41598-020-75374-1 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Thiruni N. Adikari ◽

Nasir Riaz ◽

Chathurani Sigera ◽

Preston Leung ◽

Braulio M. Valencia ◽

...

Keyword(s):

Dengue Virus ◽

Single Molecule ◽

Phylogenetic Trees ◽

Sequence Data ◽

Sequence Similarity ◽

Genetic Distances ◽

Full Length ◽

Denv Serotypes ◽

Consensus Sequences ◽

Pairwise Sequence Similarity

Abstract Current methods for dengue virus (DENV) genome amplification, amplify parts of the genome in at least 5 overlapping segments and then combine the output to characterize a full genome. This process is laborious, costly and requires at least 10 primers per serotype, thus increasing the likelihood of PCR bias. We introduce an assay to amplify near full-length dengue virus genomes as intact molecules, sequence these amplicons with third generation “nanopore” technology without fragmenting and use the sequence data to differentiate within-host viral variants with a bioinformatics tool (Nano-Q). The new assay successfully generated near full-length amplicons from DENV serotypes 1, 2 and 3 samples which were sequenced with nanopore technology. Consensus DENV sequences generated by nanopore sequencing had over 99.5% pairwise sequence similarity to Illumina generated counterparts provided the coverage was > 100 with both platforms. Maximum likelihood phylogenetic trees generated from nanopore consensus sequences were able to reproduce the exact trees made from Illumina sequencing with a conservative 99% bootstrapping threshold (after 1000 replicates and 10% burn-in). Pairwise genetic distances of within host variants identified from the Nano-Q tool were less than that of between host variants, thus enabling the phylogenetic segregation of variants from the same host.

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Characterization of the complete mitochondrial genome of Myrmus lateralis (Heteroptera, Rhopalidae) and its implication for phylogenetic analyses

ZooKeys ◽

10.3897/zookeys.1070.72742 ◽

2021 ◽

Vol 1070 ◽

pp. 13-30

Author(s):

Wanqing Zhao ◽

Dajun Liu ◽

Qian Jia ◽

Xin Wu ◽

Hufang Zhang

Keyword(s):

Phylogenetic Trees ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Purifying Selection ◽

Sister Group ◽

Start Codon ◽

Rrna Genes ◽

Trna Genes ◽

Protein Coding ◽

Inference Methods

Mitochondrial genomes (mitogenomes) are widely used in research studies on phylogenetic relationships and evolutionary history. Here, we sequenced and analyzed the mitogenome of the scentless plant bug Myrmus lateralis Hsiao, 1964 (Heteroptera, Rhopalidae). The complete 17,309 bp genome encoded 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a control region. The mitogenome revealed a high A+T content (75.8%), a positive AT-skew (0.092), and a negative GC-skew (–0.165). All 13 PCGs were found to start with ATN codons, except for cox1, in which TTG was the start codon. The Ka/Ks ratios of 13 PCGs were all lower than 1, indicating that purifying selection evolved in these genes. All tRNAs could be folded into the typical cloverleaf secondary structure, except for trnS1 and trnV, which lack dihydrouridine arms. Phylogenetic trees were constructed and analyzed based on the PCG+rRNA from 38 mitogenomes, using maximum likelihood and Bayesian inference methods, showed that M. lateralis and Chorosoma macilentum Stål, 1858 grouped together in the tribe Chorosomatini. In addition, Coreoidea and Pyrrhocoroidea were sister groups among the superfamilies of Trichophora, and Rhopalidae was a sister group to Alydidae + Coreidae.

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